Bark beetles on ice

Over the next while I plan to blog about various papers that have come out of our research program. I won’t get to all of them, obviously. But I do plan to pick and choose a few recent ones, and/or ones that have been highlights to this point in my career.

I’m going to begin with a very recent paper from my lab on bark beetle larval overwintering physiology. The paper is entitled “Global and comparative proteomic profiling of overwintering and developing mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), larvae” and is available in open access here.

Context: Mountain pine beetles usually spend their winters as small, young larvae under the bark of their host tree. In this location, they are exposed to extremely cold temperatures, sometimes ranging below –30°C and even pushing down towards -40°C. Mountain pine beetle larvae survive those temperatures by resisting freezing. Sometime in the autumn they begin to accumulate at least one antifreeze compound (glycerol) in their bodies, and then in the spring they presumably return that antifreeze compound (and perhaps others) to general metabolism for energy to complete their development

Cold temperatures have historically limited the range of the mountain pine beetle both in terms of longitude and latitude, and in terms of elevation. However, climate change has reduced the probability of cold winter temperatures – particularly the probability of extreme cold events fairly early in the autumn or fairly late in the spring. At those ‘shoulder seasons’ the larval insects have either not accumulated enough antifreeze compounds in their tissues (autumn, around Hallowe’en) or have metabolized most of it (spring, around Easter). Those are the vulnerable periods, and deep cold at those can cause populations to crash rapidly.

The lack of unseasonal cold events or of generally very deep cold in the heart of the winter over the past years has been one factor that has driven the dramatic outbreak that we’ve seen in British Columbia. In addition, historically colder areas such as the eastern slopes of the Rockies and central Alberta or high elevation areas in the Rockies have not been as cold either. This has allowed mountain pine beetles to survive winters and to move into hosts, such as jack pine and whitebark pine, that they have not historically used in the recorded past. In the case of jack pine outbreaks, the fear is that the beetle, freed from its main confine on west slope of the Rockies, is poised to move across Canada’s boreal forest. In the case of whitebark pine, the insect may further endanger already-threatened trees that are important to higher alpine ecosystems.

What we did: Up until now, the main known antifreeze compound in mountain pine beetle larva has been glycerol. We suspected that there was more to the insect’s overwintering physiology than just that, as most insects use several strategies to avoid freezing. So we conducted a proteomics experiment. That means that we surveyed the levels of all of the proteins in early-autumn larvae and compared them to levels of proteins in late-autumn larvae to look for changes. Similarly, we compared the levels of all detectable proteins between early-spring and late-spring larvae. Because we now have copious amounts of genomic data for the mountain pine beetle, we could identify which proteins did what in the insect and we could draw some conclusions as to which metabolic pathways and physiological processes were activated or deactivated in overwintering larvae at different times of the year.

What we found: In total we found 1507 proteins in all of our larval samples. Of these, 33 either increased or decreased in their levels between early- and late-autumn and 473 either increased or decreased in their levels between early- and late spring. Of the proteins that were present in either increased or decreased levels in one of the two seasons, 18 of them showed such changes in both seasons. This Venn diagram from the paper shows this general result:

 

 

These proteins can be classified into a number of general functional groups, as seen in this pie chart from the paper:

 

Of course, large groupings are not as informative as looking at individual proteins. So that is what we did, as I will write about in the next section.

What this means: In proteomics work like this, when we are dealing with hundreds of proteins, it is obvious that there is so much complexity that it would take untold pixels to explain everything. In fact, like may ‘-omics’ studies, the original authors (us, in this case) have to pick and choose things that seem interesting to them and then leave it to others wearing different research glasses to find other interesting trends. What follows are a few highlights that we noticed in the context of our research program. Our hope is that others will take our data and find other interesting things that we may have missed.

Glycerol: Our results confirm past work implicating glycerol as an important antifreeze compound in the mountain pine beetle. The data also confirm previous work in our lab (Fraser 2011, referenced in the paper) that shows certain glycerol biosynthetic genes being upregulated in the autumn and downregulated in the spring. Of particular note were the extreme variations in an enzyme called PEPCK (phosphoenolpyruvate carboxykinase) which likely indicates some level of nutritional stress in larvae heading into the cold of winter.

Trehalose: Trehalose is a major hemolymph (insect “blood”) sugar, and it has been found to be important in insect cold tolerance in other species. The levels of an enzyme involved in trehalose biosynthesis increased significantly in the autumn and decreased significantly in the spring, indicating that trehalose might function alongside glycerol as an antifreeze compound.

2-deoxyglucose: The largest autumn increases and spring decreases for any protein that we observed was for one enzyme that is involved in the biosynthesis of 2-deoxyglucose. By looking at what 2-deoxyglucose does in other organisms, we can make some guesses as to what it is doing in the mountain pine beetle. It is possible that 2-deoxyglucose regulates larval metabolism to direct energy flow appropriately toward overwintering in the autumn; that it acts in stress physiology as the insect enters a difficult period of its life; or that it is functional as an antifreeze compound. It’s also possible that it functions in more than of these roles. What is clear is that this metabolite, not previously detected in this species, is likely very important in mountain pine beetle overwintering physiology. So we have some work on our hands to figure out exactly what it’s doing.

Stress, in general: The levels of a number of proteins associated with stress physiology – for instance ferritin, superoxide dismutase and phospholipid hydroperoxide glutathione peroxidase – increased in the autumn and, in some cases, decreased again in the spring. The fact that winter is a stressful period in a mountain pine beetle’s life cycle is obvious from the basic ecology of the organism. We now have a number of stress physiology protein targets to investigate in further research.

Energy use during development: The increases and decreases of particular enzymes involved in basic metabolism indicate that mountain pine beetle larvae put most of their resources into overwintering preparation in the autumn, and only when they have survived to the spring do they begin to divert resources to ongoing developmental processes.

Detoxification of host defenses: A number of proteins commonly involved in detoxification of host chemical defenses were present in autumn larvae but, for the most part, showed reductions in the larvae as the spring progressed. Previous work in our lab has shown that larvae in the late-summer experience extremely high levels of host defense compounds. So autumn larvae are working hard to get prepared for overwintering while also dealing with a toxic environment. Once the winter is over, and the host tree is long dead, it is likely that residual host toxins have either been removed by the beetle’s symbiotic fungi or that they have naturally degraded or dissipated. In any case, the detoxification enzymes are seeming not needed to nearly the degree in the late spring that they were during the autumn. The larvae that survive living in a toxic wasteland in the autumn and that do not freeze to death in the winter are then free to use remaining stores of energy plus whatever they can glean from their host tree to complete their developmental cycle through the spring and early-summer.

Why this is important: This is the first comprehensive look at what is going on in an overwintering bark beetle. While there has been a bit of previous physiological work on mountain pine beetles and a few other bark beetle species, our work in the Tria Project has moved us into the post-genomic era for the mountain pine beetle. That means that we have an extensive genomic database and that we can conduct experiments like this that reveal the workings of a number of physiological systems all at once. We are doing other ‘-omics’ work as well on overwintering mountain pine beetle larvae, including transcriptomics (monitoring messenger RNA levels during different seasons) and directed metabolomics (monitoring specific metabolites related to overwintering) work. And we are doing experiments where we track the expression of specific genes and the activity of specific enzymes revealed to be important during this phase of the insect’s life cycle. Of course our lab, alone, can’t do all of the experimentation suggested by these results. In fact, the data are so extensive that we can’t even conceive of all of the potential experiments. That is what is cool about ‘-omics’ research – there’s no telling who will look at it and think “ah ha! I have a great idea!”

Ultimately we hope that this paper has blown the door open on bark beetle overwintering physiology. Further research is bound to uncover new and interesting results, and since winter cold and climate change play such a large role in the growth of mountain pine beetle populations, such results will help us to understand better where and how the beetles are spreading into new regions and new, susceptible hosts.

Where we are going with this: As I mentioned above, the amount of data from this one study is staggering. This is our lab’s first publication from the larger Tria Project and there are others in the works. Some of them will also produce similar copious data. Others have been designed to look at specific small portions of this study and of some of our other data. We are currently focusing in on some of the metabolic pathways and physiological processes that I mentioned above. And we hope that others are able to take our data and use it for different analyses. For instance, we have surveyed protein levels across much of the larval developmental period. Perhaps others interested in insect development will find and be able to use new information on development in the Coleoptera (beetles) generally, and in bark beetles and other weevils specifically.

This was a really fun study. We certainly hope that the data will be as useful to others as it has been for us already. This work has also moved our research program firmly into the realm of insect overwintering research, and it has been a great introduction for us into proteomics and the era of “big data” in the biological sciences.

ResearchBlogging.org

Bonnett TR, Robert JA, Pitt C, Fraser JD, Keeling CI, Bohlmann J, & Huber DP (2012). Global and comparative proteomic profiling of overwintering and developing mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), larvae. Insect biochemistry and molecular biology, 42 (12), 890-901 PMID: 22982448

Stress-free?

I am a professor. Specifically, I am a tenured associate professor at a small, Canadian, research-intensive university. And right off the bat I’d like to say that I love my job, and I love the place where I work. Since I was included as a co-author on my first paper about 17-years ago, this is the only job that I’ve wanted. I have spent countless hours in the lab and the field, with my nose in books, working as a teaching assistant, and wandering library stacks to get where I am today. Hard work was part of the equation, but there’s no denying that there was also an element of being in the right field and the right place at just the right time (maybe I’ll write about that sometime). But, in any case, I am where I am, and I love being where I am. At this point in my life, I wouldn’t trade this job for any other.

As a university professor I am granted a fair amount of research and teaching freedom, particularly now that I have attained tenure. I am able to interact with great people from across the continent and around the world in a field that I thoroughly enjoy. Working with some excellent students, postdoctoral fellows, and technicians, we have been able to build a productive and exciting research program in our lab here at UNBC. I enjoy my undergraduate teaching assignments because I find students to be inquisitive and full of great ideas. My department is very collegial and collaborative research and teaching arrangements spring up all the time.

I could go on and on. Suffice it to say, this is a great job. It’s the job that I’ve always wanted. And I consider myself extremely privileged to be in this position.

That said, it is a challenging job and one that requires continual commitment. The stress level does not reach that of, say, an air traffic controller. But it is not at all stress-free. You would be hard pressed to find a colleague of mine at any institution who wouldn’t give you an earful if you were to suggest that being a professor went hand-in-hand with having no job-related stress.

However, it seems that the folks at Forbes Magazine, reporting on a Careercast.com survey, disagree. Careercast.com and Forbes report that being a university professor is the least stressful job out there, followed by seamstresses and tailors. I was made aware of this article via a series of tweets:

 

 

 

 

…and I went over to take a look for myself.

What I found there was the same string of misconceptions about this job that I hear over and over again. Having a father who is also a professor, I have heard these “facts” from the time that I was just a young fellow. So I’m not under any illusion that the following missive will finally set the record straight, but “facts” like those found in the two articles need to be addressed somewhere. So here goes.

From the Forbes article:

“University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring.”

If I had a dime for every time that I heard this (plus a nickel for every time that I heard the “if I had a dime” cliche) I’d be able to independently fund my own research program. The fact of the matter is that university professors have pretty much the same amount of holiday time that anyone else has. I am currently allotted four weeks. Because class is in session for most of the rest of the year, I tend to take some of those vacation weeks with my family in the summer, although I haven’t taken my full four weeks in more years than I can remember. Just because class is not in session in the summer or at other times does not mean that professors are not working. The summer and reading break (Canada’s version of “spring break”) are the times that we use to get caught up on research, to write papers, to revise courses, and to read and assimilate some of the emerging literature from the past year. My research program is busier in the summer than at anytime during the rest of the year. The graduate students in our lab are not taking courses at that time, so they are free to get their thesis research done. We typically have several undergraduate summer research assistants in the lab as well. The lab hums during the summer and it’s often hard to keep up with everything.

By the end of the summer, professors need to have their course material for September ready to roll. Most professors take great pride in keeping their courses relevant and up-to-date, so summer work includes course updates and planning.

The notion that we have “a month over Christmas” is also hogwash. Yes, things do quiet down considerably between Christmas day and New Year’s. Yes, the university mainly shuts down and most faculty, administration, and staff are spending time with family for the holidays, just like most of the population of North America. But even then we need to be reachable. And most of us work up until near Christmas Eve and need to be on call during the break as well. For example, this past Christmas break I put the final editing touches on a student’s paper, I dealt with a few papers in one journal that I edit and another for which I’m an academic editor, and at one point I was doing crisis management over a fume hood in our lab that had decided to die just after Boxing Day.

I won’t bother to detail spring/reading “break” because the story is the same. Students might have the time off, but professors do not unless they use up vacation time.

“Even when school is in session they don’t spend too many hours in the classroom.”

If you are simply tracking the time spent in the classroom, then this is correct. This semester I spend seven hours of my week “in the classroom.” But anyone who takes a few moments to think about it knows that time in the classroom is not all that there is to teaching. Every lecture requires preliminary preparation. There are assignments and exams to make up and then to mark. It takes time to design meaningful assignments and to provide high-quality feedback. Students arrive in my office with great questions or to inquire about the rationale behind a mark. Office hours now extend to all hours of the day because students, rightfully in my opinion, use venues like email or Twitter to ask questions. Beyond that, any course worth teaching also takes preparation time prior to the first class session. I have never personally tallied up the amount of time that I work behind the scenes per hour of class time (frankly, I have no time to conduct such a survey), but I would bet that it comes to two or three hours of prep time per lecture hour. In a lab or tutorial courses the prep time is even more substantial.

“For tenure-track professors, there is some pressure to publish books and articles…”

This one is pure hogwash. There is not “some” pressure. Without publishing, a professor might as well be looking for a new job. My job performance (teaching, research, and service) is evaluated on a regular basis by my Department Chair, my Dean, and the upper administration. If I were to go a year without at least publishing a peer reviewed paper or two, I would receive a warning on my official report. If I were to go two years without publishing, job-related consequences would begin to kick in. And I’m speaking as a tenured professor. For a professor who has still to attain tenure, the consequences would begin to arrive much sooner.

“…but deadlines are few.”

I can’t use the word “hogwash” too much or you’d get tired of it. So I’ll stop and switch to “malarkey” instead. In most of my university committee work (service is part of our job performance evaluation) I am faced with continual deadlines. The university calendar marches on with or without me. Classes run whether or not I’m prepared. Exams are set, and final course marks need to be in within 72 hours of the final exam.

Beyond that, in my research, I am faced with deadlines in the same way that a small business owner is faced with deadlines. I do have some level of autonomy in my research program, but if I were to stop self-imposing deadlines, our lab productivity would drop, my collaborators would head off to find other colleagues to work with, and I would quickly find my research dollars drying up. Which brings up another set of deadlines – every grant that I apply for has a hard deadline. Miss the deadline, and I miss the chance at being funded.

“Working conditions tend to be cozy and civilized…”

Well, I can’t argue with this one to any great extent. I am not out in the snow and cold. I am not in a sweatshop having my human rights exploited. I am behind a desk or out in the woods measuring trees and collecting specimens. So, the article got one right. But, that said, this is no different from a plethora of other jobs out there either.

“…and there are minimal travel demands, except perhaps a non-mandatory conference or two.”

True enough, conferences are “non-mandatory.” No one is telling me that I have to attend this or that conference. But if I were to stop going to conferences I would not be keeping current with my field and I would lose some degree of contact with my colleagues. In addition, my regular annual reports to my Chair and Dean (yes, I have “bosses”) require me to report on the number of invited and regular conference presentations that the folks in our research program or I have given. Particular weight is given to invited presentations, and I find it very difficult to turn those down. Science is all about communication, and despite the boom in social media, conferences will always remain the best way to hear about, and to tell about, the most cutting-edge results.

Besides conferences, I make several collaborative trips each year as well. Due to the growing complexity of biology, for which it is becoming harder to work in isolation, more and more research funding requires the cooperation of a network of collaborators working at various scales in the system in question. One of the major parts of our current research program includes dozens of researchers from a number of institutions. Writing up research grant proposals to do this kind of work, and then ensuring that the network is functioning properly while research is ongoing, requires regular face-to-face meetings in different venues across the country. Those visits can last several days and are highly work-intensive. From the time that we sit down at the table in the morning, through our working lunches, and until we head to our hotel rooms for the night, we are constantly planning. I do not get back home after one of those meetings feeling rested. I usually feel excited by the prospects of upcoming research, but it has certainly not been a weekend at the spa.

“As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.”

Let’s score another point for Forbes here. Well, perhaps half a point. A median salary of $62,000 (this is a US median, the Canadian figures differ) is not high by any means, nor is it low compared to many other jobs. It is livable in many situations, but not all. Forbes loses half a point for adding the clause “…especially in a university town.” Not all universities are in “university towns.” Talk to professors in Vancouver, Toronto, Montreal, Calgary, Edmonton, San Francisco, New York City, or San Diego (to name a few) and ask them how far their dollar goes. Even in university towns, dollars don’t necessarily stretch too far. During a postdoctoral stint in which I was working at the USDA-Forest Service and the University of California Davis, our rent for an apartment in Davis – the epitome of an American university town – was $1300 per month. That was in 2003, and it got us what would be described as a small, modest apartment on a very busy street. An acquaintance of mine was working at Stanford University in the Bay Area at the time and was paying $1500 per month for a single room bachelor suite. This was before my wife and I had kids, so we could fit into a small apartment. Even then, it was sometimes a bit of a struggle to make ends meet on even an at-the-time decent postdoctoral salary, which was considerably less than $62,000 per year.
I realize that I’ve gone on for quite awhile here, so I’ll stop now as I’m certain that others will have more to say on this issue as well.

In summary, I love this job. There are few jobs out there that are like it. I have a great deal of autonomy to pursue interesting research and to teach courses that I enjoy. I interact with fantastic colleagues and students. I am able to spend my life learning new and interesting things about the world around us. I am continually challenged with new opportunities and exciting possibilities.

But, for the record, I do not sit in an oak-panelled office smoking my pipe after an exhausting seven-hour week of teaching. I wouldn’t even do that if my office were oak lined and if I had a pipe, because I wouldn’t have the time.

Twitter JAM

I just returned home last night after spending a few days in Edmonton at the Joint Annual Meeting of the Entomological Society of Canada and the Entomological Society of Alberta. It was a well-organized meeting with lots of great talks and posters. And, of course, lots of time to reconnect with colleagues from other universities.

A number of entomologists at the meeting, including myself, have Twitter accounts, so we “live tweeted” some of the sessions that we attended. The conference hashtag was #ESCJAM2012, in case you want to take a look at the Twitter record of the event.

From my perspective, live conference tweeting was generally a positive experience, although I say that with a few caveats. Here are my brief thoughts on the Twitter JAM:

1. I enjoyed being able to read about what was going on in other concurrent sessions. My fairly packed schedule this year did not give me much leeway to move from session to session. With so many concurrent sessions, I would have ended up missing interesting talks regardless. So it was good to have at least a taste of what was going on elsewhere. Some of the conference tweets encouraged me to talk to others about research presentations that I didn’t get to attend.

2. I can imagine how this practice is useful for professional and citizen scientists who are not able to attend a meeting. I know that if I were not at the #ESCJAM2012, I would have been following along from my office desk. I plan to virtually attend conferences like this in the future.

3. I noticed that live tweeting can be distracting in a number of ways. First, I often worried that I was causing distraction to neighbors when I would pull out my iPad to compose and send a tweet during a talk. Although I tried to sequester myself near the back edges of rooms (not great for face-to-face networking), I would sometimes get glances when my iPad lit up. Second, the act of composing and sending a tweet distracted me for a few moments from what was going on up front. There were a few times that I knew that I had missed an important point. And third, I know that a few of my followers found the stream of insect tweets to be a bit of a hassle. None of these are insurmountable, but all are issues that we need to be aware of.

4. Some tweets are better than others, including tweets at a scientific conference. Was every one of my tweets useful? I doubt it. Did every one of my tweets fairly represent the talk that I was listening to? Is that even possible in 140 characters? Obviously not. As Marshall McLuhan famously intoned, the medium is the message. Ultimately, is Twitter the best medium for science?

5. To expand on point #4, the best tweets were the ones that contained added value. A great example of this was a “toy” built by David Shorthouse that “caught” tweets with the #ESCJAM2012 hashtag and a species name and then pulled up a bunch of related references.

This is but one example of how Twitter can, in fact, punch above its 140 character weight.

In a much less technical fashion, in one or two instances I dug up new or classic papers related to a presentation and provided the URL(s) in a tweet.

Of course, that whole process took even longer than a regular tweet because I had my nose buried in Google Scholar; so we’re back at point #2. Some form of automation, perhaps similar to that also envisioned by David, could do what I did more effectively without me actually having to poke away at my iPad while only partly paying attention to someone who spent a lot of time putting together a good presentation.

6. Science is becoming more and more open, and that is a good thing. Journal articles and conferences were originally intended to increase the flow of information, ideas, and data. For many, many years both have done just that. But the web-connected world means that those vehicles don’t always do that as well as they used to in their fully traditional form; nor do they do it as well as they could considering the available technology. Just as paywalls at journal sites act to slow the flow of information compared to innovative open access options, conference travel and fees represent a paywall as well. We now have the technology to tear down those conference walls so that all of our colleagues and the general public can benefit and build on our ideas. Twitter might be part of the paywall wrecking crew, at least in the near term.

7. What if each session at a conference had a designated tweeter (DT)? Sessions already have a moderator and a projectionist, and I can imagine adding a DT to that mix. Each DT in each concurrent session would tweet into one unified conference account (e.g. @ESCJAM2012). Each session would have its own separate hashtag (e.g. #ESCforestry, #ESCbiodiversity, #ESCevolution, #ESCecology). The choice of DT for a session would be based on their interest and expertise in order to make the tweets as relevant as possible. In other words, thought would go into the choice of a session DT; the DT wouldn’t necessarily be the first available volunteer Others in the sessions would be encouraged to participate as well, but general participants would not feel like the tweeting burden was on them. General participants could maintain good focus – why even meet in person if your nose is in your device half of the time? – and could tweet from time-to-time if they felt a reason or had the expertise add value to the online conversation. But whatever the general participants decided to do, the session would be broadcast in an effective manner by an engaged and expert DT.

Do you have other thoughts on this practice? Where do you see this going in the future? Is live tweeting simply a road stop on the way to standardized full broadcasts of conferences? What, if anything, does tweeting bring to the table that is missing from face-to-face interaction or that couldn’t be realized through other non-electronic means? What hesitations to you have about this practice? How has live tweeting been a benefit to you or to others who you know?

Live tweeting, or something like it, seems to be the direction that we’re heading. It’s time for some frank discussion about the best ways to make scientific conferences more open to all. So tweet away!

Ancient hitch hikers

Any red-blooded Canadian of my approximate vintage will fondly remember reading Owl magazine (still being published!) as a kid. One of the monthly features in Owl was the “Mighty Mites.” The Mites were a group of three siblings who had the ability to shrink down to any size. They used those powers to investigate the natural world around them. I don’t remember too many of the episodes anymore, but I do recall a time when they took a wild ride on a collembolan, also known as a springtail. Since then I’ve always been interested in springtails, which are small, six-legged arthropods that are likely closely allied with insects. The Tree of Life website notes that springtails “…are probably the most abundant hexapods on Earth, with up to 250,000,000 individuals per square (sic) acre.” So, if you haven’t encountered one in your travels, it’s only because you aren’t looking.

As springtail riders, the Mighty Mites were doing what many other small creatures (including real mites) do to get around – specifically, they were being phoretic. Phoresy is when one organism hitches a ride on another organism without affecting the fitness of the organism providing the transportation.

Another group of arthropods that I’ve always been interested in are the Ephemeroptera, more commonly known as mayflies. Mayflies live most of their life cycle as aquatic nymphs in lakes and streams. Most people who spend time outdoors are familiar with large “hatches” of mayflies in the warm months of the year when myriad adult insects emerge from the water in coordinated mating dances. Among the fascinating traits common to mayflies is the fact that the adults don’t feed. In fact, their reduced mouthparts have no apparent function. Mayflies make for good trout food, and fly fishers have always worked to imitate various mayfly life stages to catch fish. The fly fishing angle – no pun intended – also partly explains my personal interest in mayflies.

Because of their life cycle traits – nymphs being restricted to the body of water in which they were hatched, and adults living only for a very short time, mainly to mate – the general view has been that mayflies really do not disperse much beyond nearby bodies of water, or perhaps along a stream course. Mayfly diversity and distribution have been explained as mainly an artifact of past continental drift. However, that view is changing, as there is evidence of at least some mayfly diversification being due to the insects somehow crossing large bodies of water.

So, mayfly dispersal and diversification is still at least partially an interesting riddle to be completely solved. And, it turns out, so is springtail dispersal. Springtails are often among the first organisms to colonize newly formed islands. How they get there has been a topic of discussion and research. And now that discussion has picked up steam because it turns out that the lives of mayflies and springtails came together in the past and may still do so today.

In a paper (Open Access) published in PLoS ONE David Penney and colleagues describe an intriguing amber fossil in which a springtail was entrapped hitched onto a mayfly via clasped antennae. The authors make a strong case for the fact that the paired fossils are not simply a chance occurrence. Among the arguments are the location of the springtail on the mayfly body; the fact that the clasped antennae are similar to those seen in an other case of fossilized collembolans hitching a ride on another arthropod (Opiliones, also known as daddy-longlegs or harvestmen, see reference in the Penney et al. 2012 PLoS ONE paper); and the lack of other springtails appearing in the sample.

This one find brings up a whole host of questions, many of which the authors suggest in their paper. For instance:

  • if we see this behavior manifested in ancient fossils, is it also happening today and why haven’t we noticed it?
  • why would springtails be adapted to hitch rides on such short-lived species that seemingly rarely travel any substantial distance?

and to that, I’d also add:

  • if we don’t see this behavior today, was there something about ancient mayfly life history or behaviors that made this association more likely? Or perhaps do those ancient mayfly traits also exist today, but we still haven’t noticed them?

Fossil evidence often makes scientists stop to consider the present day, and this is no exception to that rule. In fact, it is a great example of one field of science (entomological paleontology) passing questions on to other fields (e.g. taxonomy, animal behavior, and biogeography).

So, next summer when you see a perched mayfly minding its own business, maybe you should sneak up on it to see if it has any guests along for the ride.

ResearchBlogging.org

Penney, D., McNeil, A., Green, D., Bradley, R., Jepson, J., Withers, P., & Preziosi, R. (2012). Ancient Ephemeroptera–Collembola Symbiosis Fossilized in Amber Predicts Contemporary Phoretic Associations PLoS ONE, 7 (10) DOI: 10.1371/journal.pone.0047651

The rise of biological preprints

Although I’m not particularly long-in-the-tooth, for my entire scientific life I have known that publishers (at least in my field) do not accept papers that have been published elsewhere. And while workers in fields like mathematics and physics have long been able to post preprints of their work prior to peer review and subsequent publication in a journal, researchers in the biological sciences have generally not been allowed to do that. This is because most, if not all, journals that accept biological research manuscripts have historically considered posting a preprint as prior publication. And papers that have been previously published are, rightly, persona non grata in reputable journals.

This “prior publication” attitude toward preprints is a pity because such posting has many upsides (outlined in detail here and here and here) and very few downsides. As an editor of a small journal, and a regular reviewer for a large number of other journals in my field, I can attest to the fact that posting to such a service, in which members of the community can comment and critique an article prior to review, would have helped to strengthen just about every manuscript that has ever come across my desktop.

Some of the biggest advantages of preprint posting that I can see are:

Increased community involvement in the scientific process: Scientists at all levels would be able to take part in reading, processing, and commenting on others’ work. Amateurs would also have access to the process and could provide their often-valuable input as well. That would build community, connections, and collaborations. And that would, in turn, help to strengthen and improve the scientific endeavor in general.

Providing authors with valuable feedback and allowing them to improve their work prior to a formal review: As an editor and reviewer I understand quite intimately the (generally thankless) time and effort that it takes to process an article from first submission to final publication. As an author, I know what it feels like to have the “reject” button pressed on a study that I have invested blood and sweat into. In both cases, prior thoughtful advice and critique from the larger community would help to make the formal process smoother.

Results become visible and public more rapidly: Again, as an editor, I know how long it can take for a paper to move from submission to publication. While some traditional journals have done their best to speed things along in recent years, we all have stories of papers that have languished for eons on some editor’s or reviewer’s desk, holding up the publication of the work for even years. Preprint posting does an end-around, allowing the work to be seen immediately and reducing the irritation that slow processing by a journal might cause. The rest of the scientific community would have access to results that may improve research in other labs or even other fields prior to official acceptance and formal publication.

Less fear about being scooped: I’m thankful that my area of biology generally moves at merely a moderate clip. I’m also thankful that, in general, colleagues in my field are much more willing and eager to collaborate than to compete. However, I’m fully aware that not all fields are like this. In those fields, researchers rightly worry about another lab beating them to the punch. Preprint posting, as it is fully public, would give a researcher a claim to precedence that could be fully validated as necessary. Personally, I see this is the least important of the reasons for posting to a preprint server. But I understand that it is a consideration for many.

In the last little while many major publishers have changed their tune on this. Most recently that included the stable of journals held by the Ecological Society of America. In addition, a new kid on the block, PeerJ, is going to run a preprint service as a part of its overall open access journal offering. This is a trend that is being welcomed by many in the field. And it’s one more example of how scientific publishing is necessarily changing – I think for the better – as it is stretched by new technologies and concomitant new ways of doing things.

Whither peer review?

If you’ve been working in science long enough to have published at least one or two papers, you are already well-acquainted with certain aspects of the process:

  • Our current system of anonymous peer review has been a resounding success in terms of furthering the scientific endeavor.
  • Anonymous peer review has been around for a long time now and has carved itself a firm niche within academic culture.
  • A good reviewer is worth their weight in gold (or ink?). Their suggestions, even when graciously rejecting your article, can be used to strengthen the work for eventual publication.
  • Thankfully, most reviewers are good reviewers. Most take the time to carefully and thoughtfully train their lens of critical expertise on the submissions that they receive. In most cases, the eventual published products benefit from the (usually mainly unrewarded) referee’s effort.
  • A poor reviewer, on the other hand, is one of the most aggravating people that you will ever encounter. Poor reviewers take many forms. There are the ones that seem to have not read your paper in the first place and ask questions about things that are explicitly mentioned in your submission. There are those who seem to have an agenda, either scientific or otherwise, and who wear that agenda on their lab coat sleeve. And there are those who obviously don’t have the time or inclination to give a proper review and so either cursorily reject (usually) or accept your paper but who offer no helpful advice in their five-sentence paragraph to the editor. There is no real recourse for response; no real opportunity for dialogue. The review is the review is the review. Good, bad, ugly, or very ugly.
  • The system can be slow, not necessarily because of careful consideration by reviewers, but simply because a manuscript can sit for weeks or months on someone’s desk before they get reminded the seventeenth and final time by the journal editor to complete the review.
  • No one has ever received tenure or promotion on the basis of their careful and fair reviews of others’ articles. Conducting reviews is vital to the ongoing work of science,  but is a generally thankless job.

There are any number of peer review horror stories out there. Some of them are real. Some of them stem from the fact that nobody likes to get their work rejected. So it’s tempting to ascribe villainous motives to the anonymous reviewer(s) who stopped your article in its tracks. It is often hard to differentiate a legitimate beef from sour grapes.

Sir Winston Churchill is reputed to have said, “(i)t has been said that democracy is the worst form of government except all the others that have been tried.” And the same might be said for anonymous peer review. The fact of the matter is that peer review has served science well and continues to do so to this day. But that doesn’t mean that the current system is the pinnacle accomplishment of the scientific publishing process. Life evolves. Culture evolves. Technology evolves.

To stretch the evolutionary analogy, are we witnessing something akin to directional selective pressure on the anonymous peer review process? If so, where is the process being pushed? Are there better forms of reviewing that we have not yet tried because, until recently, our technology would not permit them? As technology changes, will peer review also change and become better – both for the scientists involved and for the furthering of our scientific knowledge in general?

Along with the recent discussion about more open science  and more “crowd” involvement in the process, we are also hearing some interesting ideas about changes to the review process. One such idea was recently presented by James Rosindell and Will Pearse at the PLoS Biologue blog:

Peer review is an essential part of science, but there are problems with the current system. Despite considerable effort on the part of reviewers and editors it remains difficult to obtain high quality, thoughtful and unbiased reviews, and reviewers are not sufficiently rewarded for their efforts. The process also takes a lot of time for editors, reviewers and authors.

And their solution:

We propose a new system for peer review. Submitted manuscripts are made immediately available online. Commissioned and/or voluntary reviews would appear online shortly afterwards. The agreement or disagreement of other interested scientists and reviewers are automatically tallied, so editors have a survey of general opinion, as well as full reviews, to inform their decisions.

In our proposed system, users would log into the system and get the opportunity to vote once for each article (or reviewers comment), thereby moving it up or down the rankings. Access could be restricted to those within the academic world or even within an appropriate discipline, so only appropriately qualified individuals could influence the rankings. The publication models of established journals would be preserved, as full publication of an article can still take place once the journal is satisfied with the scientific community’s reception of the work.

There are certainly attractive elements to this idea. First, of course, is the idea of online publication of what amounts to being a preprint. This gives the authors official priority and it gets the results out to the community as soon as possible. It also allows some semblance of “democratization” as the review process would no longer be a one-way street. And, of course, it forces reviewers to be responsible for their comments and decisions; the lack of such accountability being one of the biggest issues with the system of anonymous peer review.Referees would also receive explicit credit for their good, and not-so-good, reviews. A great reviewing track record may be the sort of thing that could actually be rewarded within the academy. There would be a real incentive to conduct good reviews.

However, I have concerns as well. Just as with “liking” on Facebook, this has the potential to become a popularity contest. And science is not about popularity. It is about truth. And truth can come from unpopular sources. There is also the likelihood that some researchers in highly competitive fields will only sign on to such a system with extreme reluctance due to the fear of being scooped.

Beyond that, would already overworked researchers really take quality time to thoughtfully comment on preprints? And, would there be ways to game the system, analogous to people trying to increase their search engine rankings? Finally, what about small and boutique journals? The authors of the new peer review proposal envision a marketplace where editors bid for articles within the ranking system. As the editor of a small, regional journal, I am worried about what would happen to journals like the one that I oversee. Would we be able to win bids for quality papers? Or would we get lost in the shuffle after over 100 years of service to the scientific community?

As with the shifts that are occurring with the move toward open access and away from impact factors, I am positive that peer review will also have to change. And it’s good to see that people are thinking about how those changes will come about. Hopefully some of the various concerns with the intended and unintended consequences of changing the system will also be thoughtfully considered. There’s nothing wrong with moving quickly as long as you apply the brakes appropriately around the corners.

A quick post script: It should be noted that the peer review process is not a monolithic edifice of utter similarity across the board. Some journals (e.g., BMJ) have been practicing open peer review for quite some time now. And some new journals (e.g. PeerJ) are also pushing into new territory on this front.

Good news x 3

Most days environmental news is bleak to say the least. Truthfully, much of what’s going on is bleak. Species are going extinct at record rates. Climate change seems to be accelerating. Environmental degradation is having real effects on real people.

But even though the bad news is usually what makes it onto the evening news, there are bits and pieces of good news as well. And those deserve to be highlighted. So, let’s take a look at three of those today.

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A clawed cave spider: I always get excited when I hear about new species discoveries. That’s partly because it reminds me that no matter how much we think that we’ve figured out, there are still zillions of cool things out there that we have no clue about. We just need to look – sometimes in difficult places. In this case, the cool new find is a new species of spider, Trogloraptor marchingtoni. And not just a new species, but seemingly an entirely new family. If a new species is a big deal, a new family is an even bigger deal. By way of analogy ostriches, pelicans, and hummingbirds are each in separate bird families. So you might say that this newly discovered spider is approximately as different from other groups of spiders as those three groups of birds are from each other.

Trogloraptor is about 4 cm in diameter and lives mainly in caves and some old growth forests. It has substantial claws on its legs, but it is not clear what they are used for. And, now that we know about this creature there are a ton of other new and interesting things to find out as well. What will those discoveries be? Only time, and more hard work, will tell.

An (un)extinct snail: The Mobile River Basin in the southeastern United States is home to an amazing diversity of freshwater mollusks. Or perhaps it should be said that it was home to an amazing diversity of freshwater mollusks. After years of human influences, several dozen species are now extinct. However, in a recent survey of the snail fauna of the Cahaba River, researchers found a small population of a snail that has been thought to be extinct for decades. The snails can be bred in captivity and the authors of the linked research article point out several locations that may be suitable for reintroductions.

Monarch butterflies finally find protection: I’ll probably devote an entire post to monarch butterflies in the near future because they are so amazing. Briefly, these insects migrate across a huge swath of North America to a few very small wintering areas in forest groves the mountains of Mexico. So, entire populations that cover large chunks of geography in the summer are dependent upon a the survival of a few hectares of trees. Because of this, they are highly susceptible to deforestation in that region. Illegal logging has been impinging on these winter redoubts for decades. Removal of trees, even trees not used by the butterflies for roosting, allows more rain below the canopy. Wet butterflies are highly susceptible to winter cold.

The whole situation has been extremely dire in recent years. But now comes news that cooperative work between government, NGOs, private individuals, and the people who live near to the butterflies’ overwintering groves has almost completely eliminated illegal logging. Residents are now replanting trees in the butterfly groves and are working on developing a more robust ecotourism-based economy.

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Yes, there are spots of good news out there as well. It pays to look for them because we need to take the time to highlight these events and accomplishments. They are due in large part to the dedication and efforts of researchers and, as exemplified in the case of the monarchs, to the people who are most likely to be affected by the negative consequences of doing nothing.

Slow science

I have an admission to make. All the way through my Ph.D. studies and on into my first postdoctoral stint, I had no idea what an impact factor was. I still remember my first encounter with the concept. A number of fellow postdocs and students were discussing which journal a particular paper that one of them was working on should be sent to. After a bit of listening (and probably nodding along cluelessly with the discussion) I found a computer and looked it up. Most of you reading this probably know what it is. But, for the record, it is a measure of how many times recent articles in a given journal are cited compared to recent articles in other journals. And this is supposed to allow ranking of a specific journal’s importance compared to others. Of course, this whole endeavor is fraught with problems. But even so, it’s become well nigh impossible to hold an extended conversation about academic publishing with a group of scientists without impact factor considerations coming up.

I have another admission to make. Until I began the process of applying for tenure awhile back I had never heard of an h-index. Suddenly I found it was as vital to my academic life as is the oxygen level in my blood to my real life. So, off I went to Google Scholar where I found that not only was my (decent, but somewhat modest) h-index calculated for me, but so was my i10-index. I hesitate to bore you with details, but in case you don’t know what these are and really need the information here you go…

To calculate your h-index, put your papers in order from most cited to least cited. Then count down the ranked papers from top to bottom until you get to the last point where a paper has at least as many citations as its rank on the list. That is your h-index.

An i10-index is simpler – it’s the number of your papers with at least 10 citations.

Both of these are influenced by age or, more precisely, academic age (how long you’ve been in the game) and by how much other people make use of your findings in their own work.

To a science outsider these measures might sound a bit odd. But despite their issues they are now the standard for how university administrators, granting agencies, and others judge academic work. For better or for worse scientists and their publications are now part of a Google-sized numbers game.

Is it in the best interests of science, and society, that measures like this are the yardsticks used to judge scientific worth? Joern Fischer, Euan Ritchie, and Jan Hanspach argue a persuasive “no” to that question in a short opinion piece in TREE (27:473-474) entitled “Academia’s obsession with quantity.” They explain that, among other things, the quantity obsession is concentrating huge amounts of resources among a small cadre of large research groups. And the push for speedy publication in high-impact journals is forcing a focus on fast and shallow rather than reflective thought, deep experimentation, and patient observation. Careful lab research and long-term field studies are taking a back seat to expedient and efficient – but ultimately less satisfying – answers. Beyond that, and arguably more importantly, the love of indices is hurting the families and other relationships of academics.

To quote Fisher et al.: “(the) modern mantra of quantity is taking a heavy toll on two prerequisites for generating wisdom: creativity and reflection.”

Charles Darwin’s voyage on the Beagle lasted from 1837 to 1839. “On the Origin of Species” was published in 1859, twenty years after the boat had docked, and then only under duress as Alfred Wallace was hot on the same trail.

Gregor Mendel published his important work on the transmission of traits in a little known journal. His work only saw the light of day years later when the rest of the world had basically caught up with his ideas.

Both of these individuals, and many others of their day, were methodical, thoughtful, and not in a rush to publish. If Darwin had been alive today, he would have had pressure to put out several papers before he even got off of the ship. His granting agency would have expected him to “meet milestones,” “accomplish outcomes,” and fill out innumerable Gantt charts on a semi-quarterly basis. He would have spent most of his days responding to emails rather than collecting specimens.

Mendel’s supervisor would have been asking him “why on earth would you want to publish in that journal?” And the editor of the high-impact journal that received his work probably would have written back “Peas? Are you serious?”

But without the methodical research of the past – and by “past” we barely have to go back much more than a decade or so to see slower science – where would be we today? Does our newly hyper-caffeinated research world really work better than the more contemplative system of Mendel, Wallace, and Darwin? Is there some happy medium that we can all agree on?

I would argue that things are starting to change. Just like the music industry was finally forced to change in recent years, technology is going to force academia to change as well. In great part this is due to the rise of open access journals. These journals – such as offerings from PLoS, eLife, PeerJ, F1000 Research, and Ecosphere – are changing the publishing landscape. And the academic world will have little choice but to move along in step. Thankfully, much of the academic rank and file is quite happy to jump on board this particular train. Besides offering research results – which were likely paid for with public money – to the public for free, these journals also offer article-level metrics. That means that instead of a journal-wide impact factor, each article can be assessed by the number of downloads and/or citations. Many of these journals also promise to publish all rigorous research that passes peer review no matter how “sexy” it seems to be at the moment. So, if someone takes the time and effort for careful research on pea genetics, they can get it published even if much of the world currently could care less about peas. The crowd gets to decide – either immediately or over time – if the findings are worth the electrons that light up the pixels on their devices.

It is starting to look like this is another case of “the more things change, the more they (return to) the same.” Just as it seemed that letter writing was dying, in came email. And now, just as it seems that contemplative science and judgement of the merit of single works were going out the window, along comes the open access publishing paradigm.

These open access endeavors deserve our support. And I am looking forward to seeing where this takes us in the coming years.